OpenRaiser/Intern-Atlas huggingface dataset:
Benchmarking LLMs for Pairwise Causal Discovery in Biomedical and Multi-Domain Contexts
Venue: arXiv cs.CL 2026
Year: 2026

The safe deployment of large language models (LLMs) in high-stakes fields like biomedicine, requires them to be able to reason about cause and effect. We investigate this ability by testing 13 open-source LLMs on a fundamental task: pairwise causal discovery (PCD) from text. Our benchmark, using 12 diverse datasets, evaluates two core skills: 1) \textbf{Causal Detection} (identifying if a text contains a causal link) and 2) \textbf{Causal Extraction} (pulling out the exact cause and effect phrases). We tested various prompting methods, from simple instructions (zero-shot) to more complex strategies like Chain-of-Thought (CoT) and Few-shot In-Context Learning (FICL). The results show major deficiencies in current models. The best model for detection, DeepSeek-R1-Distill-Llama-70B, only achieved a mean score of 49.57\% ($C_{detect}$), while the best for extraction, Qwen2.5-Coder-32B-Instruct, reached just 47.12\% ($C_{extract}$). Models performed best on simple, explicit, single-sentence relations. However, performance plummeted for more difficult (and realistic) cases, such as implicit relationships, links spanning multiple sentences, and texts containing multiple causal pairs. We provide a unified evaluation framework, built on a dataset validated with high inter-annotator agreement ($κ\ge 0.758$), and make all our data, code, and prompts publicly available to spur further research. \href{https://github.com/sydneyanuyah/CausalDiscovery}{Code available here: https://github.com/sydneyanuyah/CausalDiscovery}
The Rise of Large Language Models and the Direction and Impact of US Federal Research Funding
Venue: arXiv cs.DL 2026
Year: 2026

Federal research funding shapes the direction, diversity, and impact of the US scientific enterprise. Large language models (LLMs) are rapidly diffusing into scientific practice, holding substantial promise while raising widespread concerns. Despite growing attention to AI use in scientific writing and evaluation, little is known about how the rise of LLMs is reshaping the public funding landscape. Here, we examine LLM involvement at key stages of the federal funding pipeline by combining two complementary data sources: confidential National Science Foundation (NSF) and National Institutes of Health (NIH) proposal submissions from two large US R1 universities, including funded, unfunded, and pending proposals, and the full population of publicly released NSF and NIH awards. We find that LLM use rises sharply beginning in 2023 and exhibits a bimodal distribution, indicating a clear split between minimal and substantive use. Across both private submissions and public awards, higher LLM involvement is consistently associated with lower semantic distinctiveness, positioning projects closer to recently funded work within the same agency. The consequences of this shift are agency-dependent. LLM use is positively associated with proposal success and higher subsequent publication output at NIH, whereas no comparable associations are observed at NSF. Notably, the productivity gains at NIH are concentrated in non-hit papers rather than the most highly cited work. Together, these findings provide large-scale evidence that the rise of LLMs is reshaping how scientific ideas are positioned, selected, and translated into publicly funded research, with implications for portfolio governance, research diversity, and the long-run impact of science.
MARS: Unleashing the Power of Speculative Decoding via Margin-Aware Verification
Venue: arXiv cs.LG 2026
Year: 2026

Speculative Decoding (SD) accelerates autoregressive large language model (LLM) inference by decoupling generation and verification. While recent methods improve draft quality by tightly coupling the drafter with the target model, the verification mechanism itself remains largely unchanged, relying on strict token-level rejection sampling. In practice, modern LLMs frequently operate in low-margin regimes where the target model exhibits weak preference among top candidates. In such cases, rejecting plausible runner-up tokens yields negligible information gain while incurring substantial rollback cost, leading to a fundamental inefficiency in verification. We propose Margin-Aware Speculative Verification, a training-free and domain-agnostic verification strategy that adapts to the target model's local decisiveness. Our method conditions verification on decision stability measured directly from the target logits and relaxes rejection only when strict verification provides minimal benefit. Importantly, the approach modifies only the verification rule and is fully compatible with existing target-coupled speculative decoding frameworks. Extensive experiments across model scales ranging from 8B to 235B demonstrate that our method delivers consistent and significant inference speedups over state-of-the-art baselines while preserving generation quality across diverse benchmarks.
SAGE-FM: A lightweight and interpretable spatial transcriptomics foundation model
Venue: arXiv cs.LG 2026
Year: 2026

Spatial transcriptomics enables spatial gene expression profiling, motivating computational models that capture spatially conditioned regulatory relationships. We introduce SAGE-FM, a lightweight spatial transcriptomics foundation model based on graph convolutional networks (GCNs) trained with a masked central spot prediction objective. Trained on 416 human Visium samples spanning 15 organs, SAGE-FM learns spatially coherent embeddings that robustly recover masked genes, with 91% of masked genes showing significant correlations (p < 0.05). The embeddings generated by SAGE-FM outperform MOFA and existing spatial transcriptomics methods in unsupervised clustering and preservation of biological heterogeneity. SAGE-FM generalizes to downstream tasks, enabling 81% accuracy in pathologist-defined spot annotation in oropharyngeal squamous cell carcinoma and improving glioblastoma subtype prediction relative to MOFA. In silico perturbation experiments further demonstrate that the model captures directional ligand-receptor and upstream-downstream regulatory effects consistent with ground truth. These results demonstrate that simple, parameter-efficient GCNs can serve as biologically interpretable and spatially aware foundation models for large-scale spatial transcriptomics.
Controllable Layered Image Generation for Real-World Editing
Venue: arXiv cs.CV 2026
Year: 2026

Recent image generation models have shown impressive progress, yet they often struggle to yield controllable and consistent results when users attempt to edit specific elements within an existing image. Layered representations enable flexible, user-driven content creation, but existing approaches often fail to produce layers with coherent compositing relationships, and their object layers typically lack realistic visual effects such as shadows and reflections. To overcome these limitations, we propose LASAGNA, a novel, unified framework that generates an image jointly with its composing layers--a photorealistic background and a high-quality transparent foreground with compelling visual effects. Unlike prior work, LASAGNA efficiently learns correct image composition from a wide range of conditioning inputs--text prompts, foreground, background, and location masks--offering greater controllability for real-world applications. To enable this, we introduce LASAGNA-48K, a new dataset composed of clean backgrounds and RGBA foregrounds with physically grounded visual effects. We also propose LASAGNABENCH, the first benchmark for layer editing. We demonstrate that LASAGNA excels in generating highly consistent and coherent results across multiple image layers simultaneously, enabling diverse post-editing applications that accurately preserve identity and visual effects. LASAGNA-48K and LASAGNABENCH will be publicly released to foster open research in the community. The project page is https://rayjryang.github.io/LASAGNA-Page/.
AdversaRiskQA: An Adversarial Factuality Benchmark for High-Risk Domains
Venue: arXiv cs.CL 2026
Year: 2026

Hallucination in large language models (LLMs) remains an acute concern, contributing to the spread of misinformation and diminished public trust, particularly in high-risk domains. Among hallucination types, factuality is crucial, as it concerns a model's alignment with established world knowledge. Adversarial factuality, defined as the deliberate insertion of misinformation into prompts with varying levels of expressed confidence, tests a model's ability to detect and resist confidently framed falsehoods. Existing work lacks high-quality, domain-specific resources for assessing model robustness under such adversarial conditions, and no prior research has examined the impact of injected misinformation on long-form text factuality. To address this gap, we introduce AdversaRiskQA, the first verified and reliable benchmark systematically evaluating adversarial factuality across Health, Finance, and Law. The benchmark includes two difficulty levels to test LLMs' defensive capabilities across varying knowledge depths. We propose two automated methods for evaluating the adversarial attack success and long-form factuality. We evaluate six open- and closed-source LLMs from the Qwen, GPT-OSS, and GPT families, measuring misinformation detection rates. Long-form factuality is assessed on Qwen3 (30B) under both baseline and adversarial conditions. Results show that after excluding meaningless responses, Qwen3 (80B) achieves the highest average accuracy, while GPT-5 maintains consistently high accuracy. Performance scales non-linearly with model size, varies by domains, and gaps between difficulty levels narrow as models grow. Long-form evaluation reveals no significant correlation between injected misinformation and the model's factual output. AdversaRiskQA provides a valuable benchmark for pinpointing LLM weaknesses and developing more reliable models for high-stakes applications.
Securing LLM-as-a-Service for Small Businesses: An Industry Case Study of a Distributed Chatbot Deployment Platform
Venue: arXiv cs.DC 2026
Year: 2026

Large Language Model (LLM)-based question-answering systems offer significant potential for automating customer support and internal knowledge access in small businesses, yet their practical deployment remains challenging due to infrastructure costs, engineering complexity, and security risks, particularly in retrieval-augmented generation (RAG)-based settings. This paper presents an industry case study of an open-source, multi-tenant platform that enables small businesses to deploy customised LLM-based support chatbots via a no-code workflow. The platform is built on distributed, lightweight k3s clusters spanning heterogeneous, low-cost machines and interconnected through an encrypted overlay network, enabling cost-efficient resource pooling while enforcing container-based isolation and per-tenant data access controls. In addition, the platform integrates practical, platform-level defences against prompt injection attacks in RAG-based chatbots, translating insights from recent prompt injection research into deployable security mechanisms without requiring model retraining or enterprise-scale infrastructure. We evaluate the proposed platform through a real-world e-commerce deployment, demonstrating that secure and efficient LLM-based chatbot services can be achieved under realistic cost, operational, and security constraints faced by small businesses.
Resource Allocation and Sharing for UAV-Assisted Integrated TN-NTN with Multi-Connectivity
Venue: arXiv cs.NI 2026
Year: 2026

Unmanned aerial vehicles (UAVs) with multi-connectivity (MC) capabilities efficiently and reliably transfer data between terrestrial networks (TNs) and non-terrestrial networks (NTNs). However, optimally sharing and allocating spectrum and power resources to maintain MC while ensuring reliable connectivity and optimal performance remains challenging in such networks. Channel variations induced by mobility in UAV networks, coupled with the varying quality of service (QoS) demands of heterogeneous devices, resource sharing, and fairness requirements in capacity distribution pose challenges to optimal resource allocation. Thus, this paper investigates resource allocation for QoS-constrained, MC-enabled, dynamic UAVs in an integrated TN-NTN environment with spectrum sharing and fairness considerations. To this end, we consider three types of links: UAV-to-radio base station (RBS), UAV-to-UAV, and UAV-to-HAP. We also assume two types of UAVs with diverse QoS requirements to reflect a practical scenario. Consequently, we propose two algorithms. The first algorithm maximizes the capacity of UAVs-RBS and UAVs-HAP links while ensuring the reliability of the UAV-UAV link. To achieve this, the algorithm maximizes the collective throughput of the UAVs by optimizing the sum capacity of all the UAV-RBS and UAV-HAP links. Next, to provide constant capacity to all links and ensure fairness, we propose another algorithm that maximizes the minimum capacity across all links. We validate the performance of both algorithms through simulation
ALIGNAgent: Adaptive Learner Intelligence for Gap Identification and Next-step guidance
Venue: arXiv cs.AI 2026
Year: 2026

Personalized learning systems have emerged as a promising approach to enhance student outcomes by tailoring educational content, pacing, and feedback to individual needs. However, most existing systems remain fragmented, specializing in either knowledge tracing, diagnostic modeling, or resource recommendation, but rarely integrating these components into a cohesive adaptive cycle. In this paper, we propose ALIGNAgent (Adaptive Learner Intelligence for Gap Identification and Next-step guidance), a multi-agent educational framework designed to deliver personalized learning through integrated knowledge estimation, skill-gap identification, and targeted resource recommendation.ALIGNAgent begins by processing student quiz performance, gradebook data, and learner preferences to generate topic-level proficiency estimates using a Skill Gap Agent that employs concept-level diagnostic reasoning to identify specific misconceptions and knowledge deficiencies. After identifying skill gaps, the Recommender Agent retrieves preference-aware learning materials aligned with diagnosed deficiencies, implementing a continuous feedback loop where interventions occur before advancing to subsequent topics. Extensive empirical evaluation on authentic datasets from two undergraduate computer science courses demonstrates ALIGNAgent's effectiveness, with GPT-4o-based agents achieving precision of 0.87-0.90 and F1 scores of 0.84-0.87 in knowledge proficiency estimation validated against actual exam performance.
BanditLP: Large-Scale Stochastic Optimization for Personalized Recommendations
Venue: arXiv cs.LG 2026
Year: 2026

We present BanditLP, a scalable multi-stakeholder contextual bandit framework that unifies neural Thompson Sampling for learning objective-specific outcomes with a large-scale linear program for constrained action selection at serving time. The methodology is application-agnostic, compatible with arbitrary neural architectures, and deployable at web scale, with an LP solver capable of handling billions of variables. Experiments on public benchmarks and synthetic data show consistent gains over strong baselines. We apply this approach in LinkedIn's email marketing system and demonstrate business win, illustrating the value of integrated exploration and constrained optimization in production.
Enhanced Convergence in p-bit Based Simulated Annealing with Partial Deactivation for Large-Scale Combinatorial Optimization Problems
Venue: arXiv cs.ET 2026
Year: 2026

This article critically investigates the limitations of the simulated annealing algorithm using probabilistic bits (pSA) in solving large-scale combinatorial optimization problems. The study begins with an in-depth analysis of the pSA process, focusing on the issues resulting from unexpected oscillations among p-bits. These oscillations hinder the energy reduction of the Ising model and thus obstruct the successful execution of pSA in complex tasks. Through detailed simulations, we unravel the root cause of this energy stagnation, identifying the feedback mechanism inherent to the pSA operation as the primary contributor to these disruptive oscillations. To address this challenge, we propose two novel algorithms, time average pSA (TApSA) and stalled pSA (SpSA). These algorithms are designed based on partial deactivation of p-bits and are thoroughly tested using Python simulations on maximum cut benchmarks that are typical combinatorial optimization problems. On the 16 benchmarks from 800 to 5,000 nodes, the proposed methods improve the normalized cut value from 0.8% to 98.4% on average in comparison with the conventional pSA.
Computational Complexity of Physical Counting
Venue: arXiv cs.CC 2026
Year: 2026

We characterize which coordinates of a factored state space determine optimal actions. For $\mathcal{D}=(A,S,U)$ with $S=X_1\times\cdots\times X_n$, coordinate set $I$ is sufficient if $s_I=s'_I\Rightarrow\operatorname{Opt}(s)=\operatorname{Opt}(s')$. The decision quotient $Q=S/{\sim}$ ($s\sim s'\Leftrightarrow\operatorname{Opt}(s)=\operatorname{Opt}(s')$) is the minimal abstraction: any abstraction preserving optimal actions factors uniquely through $Q$. We prove fourteen first-principles theorems (thirteen from pure mathematics, one empirical). The chain from counting measure to probability to Bayes' theorem to $Q$ follows from finite set cardinality. Fisher information, entropy, optimal transport, rate-distortion, and thermodynamics each independently recover $\mathrm{srank}$ as decision complexity measure. From $\log x\leq x-1$ alone, Bayesian updating uniquely minimizes expected log loss. Complexity: SUFFICIENCY-CHECK and MINIMUM-SUFFICIENT-SET are coNP-complete; ANCHOR-SUFFICIENCY is $Σ_2^P$-complete; stochastic and sequential variants PP- and PSPACE-complete with strict separation. Six subcases admit polynomial algorithms. Under ETH, succinct encodings carry $2^{Ω(n)}$ lower bounds. Verification requires $\geq 2^{n-1}$ witness pairs. Two results carry empirical conditions. Conditional on Landauer's principle ($k_BT\ln 2$ per bit erasure; experimentally confirmed 2012), $dU\geqλ\,dC$ follows by composition with bit-operation bounds; rejecting it requires rejecting Landauer. Conditional on stochastic thermodynamics (Barato--Seifert 2015), $\mathrm{Var}(J)/\langle J\rangle^2\geq 2/σ$ bounds decision precision by entropy production, minimal $σ$ scaling with $\mathrm{srank}$.
Parallelism and Generation Order in Masked Diffusion Language Models: Limits Today, Potential Tomorrow
Venue: arXiv cs.CL 2026
Year: 2026

Masked Diffusion Language Models (MDLMs) promise parallel token generation and arbitrary-order decoding, yet it remains unclear to what extent current models truly realize these capabilities. We characterize MDLM behavior along two dimensions -- parallelism strength and generation order -- using Average Finalization Parallelism (AFP) and Kendall's tau. We evaluate eight mainstream MDLMs (up to 100B parameters) on 58 benchmarks spanning knowledge, reasoning, and programming. The results show that MDLMs still lag behind comparably sized autoregressive models, mainly because parallel probabilistic modeling weakens inter-token dependencies. Meanwhile, MDLMs exhibit adaptive decoding behavior: their parallelism and generation order vary significantly with the task domain, the stage of reasoning, and whether the output is correct. On tasks that require "backward information" (e.g., Sudoku), MDLMs adopt a solution order that tends to fill easier Sudoku blanks first, highlighting their advantages. Finally, we provide theoretical motivation and design insights supporting a Generate-then-Edit paradigm, which mitigates dependency loss while retaining the efficiency of parallel decoding.
Tackling the Scaffolding Paradox: A Person-Centered Adaptive Robotic Interview Coach
Venue: arXiv cs.HC 2026
Year: 2026

Job interview anxiety is a prevalent challenge among university students and can undermine both performance and confidence in high-stakes evaluative situations. Social robots have shown promise in reducing anxiety through emotional support, yet how such systems should balance psychological safety with effective instructional guidance remains an open question. In this work, we present a three-phase iterative design study of a robotic interview coach grounded in Person-Centered Therapy (PCT) and instructional scaffolding theory. Across three weekly sessions (N=8), we systematically explored how different interaction strategies shape users' emotional experience, cognitive load, and perceived utility. Phase I demonstrated that a PCT-based robot substantially increased perceived psychological safety but introduced a Safety-Guidance Gap, in which users felt supported yet insufficiently coached. Phase II revealed a Scaffolding Paradox: immediate feedback improved clarity but disrupted conversational flow and increased cognitive load, whereas delayed feedback preserved realism but lacked actionable specificity. To resolve this tension, Phase III introduced an Agency-Driven Interaction Mode that allowed users to opt in to feedback dynamically. Qualitative findings indicated that user control acted as an anxiety buffer, restoring trust, reducing overload, and reframing the interaction as collaborative rather than evaluative. Quantitative measures further showed significant reductions in interview-related social and communication anxiety, while maintaining high perceived warmth and therapeutic alliance. We synthesize these findings into an Adaptive Scaffolding Ecosystem framework, highlighting user agency as a key mechanism for balancing emotional support and instructional guidance in social robot coaching systems.
Generative AI-Empowered Semantic Twin Channel Model for ISAC
Venue: arXiv cs.IT 2026
Year: 2026

Integrated sensing and communication (ISAC) increasingly exposes a gap in today's channel modeling. Efficient statistical models focus on coarse communication-centric metrics, and therefore miss the weak but critical multipath signatures for sensing, whereas deterministic models are computationally inefficient to scale for system-level ISAC evaluation. This gap calls for a unifying abstraction that can couple what the environment means for sensing with how the channel behaves for communication, namely, environmental semantics. This article clarifies the meaning and essentiality of environmental semantics in ISAC channel modeling and establishes how semantics is connected to observable channel structures across multiple semantic levels. Based on this perspective, a semantics-oriented channel modeling principle was advocated, which preserves environmental semantics while abstracting unnecessary detail to balance accuracy and complexity. Then, a generative AI-empowered semantic twin channel model (STCM) was introduced to generate a family of physically plausible channel realizations representative of a semantic condition. Case studies further show semantic consistency under challenging multi-view settings, suggesting a practical path to controllable simulation, dataset generation, and reproducible ISAC benchmarking toward future design and standardization.